Parameters to makefile - outputs samples

doc/user_manual/makefile

-EXAMPLE_DIR = ~/INSTALL_DIR/SPELL_TEST/spell_qtl-0.1-alpha.1-Linux/share/spell-qtl/examples/three_parents_F2
+BINDIR = /home/sjasson/INSTALL_DIR/SPELL_TEST/spell_qtl-0.1-alpha.1-Linux/bin
+SRCDIR = /home/sjasson/dev/spel
+
+
+EXAMPLE_DIR = $(SRCDIR)/examples/three_parents_F2
 
 user_manual.pdf : spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg inputs outputs
 	pdflatex --shell-escape user_manual.tex && pdflatex --shell-escape user_manual.tex
@@ -6,20 +10,20 @@ user_manual.pdf : spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-ex
 version.tex :
 	git tag | tail -1 > version.tex
 
-spell-pedigree.tex : ../man/spell-pedigree.1.md
-	/usr/bin/pandoc ../man/spell-pedigree.1.md --listings -f markdown -t latex -o spell-pedigree.tex
+spell-pedigree.tex : $(SRCDIR)/doc/man/spell-pedigree.1.md
+	/usr/bin/pandoc $(SRCDIR)/doc/man/spell-pedigree.1.md --listings -f markdown -t latex -o spell-pedigree.tex
 	sed -i s/\\label\{/\label\{spell-pedigree:/g spell-pedigree.tex
 
-spell-marker.tex : ../man/spell-marker.1.md
-	/usr/bin/pandoc ../man/spell-marker.1.md --listings -f markdown -t latex -o spell-marker.tex
+spell-marker.tex : $(SRCDIR)/doc/man/spell-marker.1.md
+	/usr/bin/pandoc $(SRCDIR)/doc/man/spell-marker.1.md --listings -f markdown -t latex -o spell-marker.tex
 	sed -i s/\\label\{/\label\{spell-marker:/g spell-marker.tex
 
 spell-qtl.tex : ../man/spell-qtl.1.md
-	/usr/bin/pandoc ../man/spell-qtl.1.md --listings -f markdown -t latex -o spell-qtl.tex
+	/usr/bin/pandoc $(SRCDIR)/doc/man/spell-qtl.1.md --listings -f markdown -t latex -o spell-qtl.tex
 	sed -i s/\\label\{/\label\{spell-qtl:/g spell-qtl.tex
 
-spell-qtl-examples.tex : ../man/spell-qtl-examples.1.md
-	/usr/bin/pandoc ../man/spell-qtl-examples.1.md --listings -f markdown -t latex -o spell-qtl-examples.tex
+spell-qtl-examples.tex : $(SRCDIR)/doc/man/spell-qtl-examples.1.md
+	/usr/bin/pandoc $(SRCDIR)/doc/man/spell-qtl-examples.1.md --listings -f markdown -t latex -o spell-qtl-examples.tex
 	sed -i s/\\label\{/\label\{spell-qtl-examples:/g spell-qtl-examples.tex
 
 
@@ -32,9 +36,9 @@ inputs :
 
 
 outputs :
-	spell-pedigree -wd my_directory -n my_name -p $(EXAMPLE_DIR)/example1.ped
-	spell-marker -wd my_directory -n my_name -m F2:A/B $(EXAMPLE_DIR)/example1_F2.gen -m F2C:A/C $(EXAMPLE_DIR)/example1_F2C.gen -o F2,F2C -O1
-	#spell-qtl -wd my_directory -n my_name  -p F2 $(EXAMPLE_DIR)/example1_F2.phen -p F2C $(EXAMPLE_DIR)/example1_F2C.phen -gm $(EXAMPLE_DIR)/example1.map -P auto QTL-detection CIM connected
+	$(BINDIR)/spell-pedigree -wd my_directory -n my_name -p $(EXAMPLE_DIR)/example1.ped
+	$(BINDIR)/spell-marker -wd my_directory -n my_name -m F2:A/B $(EXAMPLE_DIR)/example1_F2.gen -m F2C:A/C $(EXAMPLE_DIR)/example1_F2C.gen -o F2,F2C -O1 -Op
+	$(BINDIR)/spell-qtl -wd my_directory -n my_name  -p F2 $(EXAMPLE_DIR)/example1_F2.phen -p F2C $(EXAMPLE_DIR)/example1_F2C.phen -gm $(EXAMPLE_DIR)/example1.map output-nppop
 
 clean:
 	rm -f *.aux *.log *.pdf *.toc *.out *.lol

doc/user_manual/user_manual.tex

@@ -458,22 +458,34 @@ General output directory organization is  :
     %s sep=12pt,
     before computing xy={l=20pt},
   }
-[my\_directory
-	[my\_name.1-point
+[my\_directory \textsl{(directory)}
+	[my\_name.1-point \textsl{(directory)}
+		[my\_name.pedigree-and-probabilities.M\_1\_10.csv \textsl{(text file)} ]
 		[...]
 	]
-	[my\_name.cache
-		[my\_name.spell-marker.data]
-		[my\_name.spell-pedigree.data]
-		[...]
+	[my\_name.cache \textsl{(directory)}
+		[my\_name.spell-marker.data \textsl{(binary file)}]
+		[my\_name.spell-pedigree.data \textsl{(binary file)}]
 	]
-	[my\_name.n-point
-		[...]
+	[my\_name.n-point \textsl{(directory)}
+		[ch1 \textsl{(directory)}
+			[F2 \textsl{(directory)}
+				[my\_name.ch1.F2.0.csv \textsl{(text file)}]
+				[...]
+			]
+			[F2C \textsl{(directory)}
+				[my\_name.ch1.F2.0.csv \textsl{(text file)}]
+				[...]
+			]
+		]
+		[ch2 \textsl{(directory)}
+			[...]
+		]
 	]
-	[my\_name.report
+	[my\_name.report \textsl{(directory)}
 		[...]
 	]
-	[my\_name.spell-qtl.log
+	[my\_name.spell-qtl.log \textsl{(text file)} 
 	]
 ]
 \end{forest}
@@ -484,8 +496,8 @@ General output directory organization is  :
 \item A configuration name using command line option \texttt{-n my\_name} or \texttt{--name my\_name} is used to name subdirectories.
 \item Parental Origin Probabilities are output as CSV files
 \begin{description}
-\item [1-point] one file per marker (with pedigree like structure),
-\item [n-point] one file per linkage group per generation per individual
+\item [1-point] one file per marker (with pedigree like structure), use option \texttt{-O1} in command \texttt{spell-marker} to output these files
+\item [n-point] one file per linkage group per generation per individual, use model option \texttt{output-nppop} in command \texttt{spell-qtl} to output these files. 
 \end{description}
 \item a report containing
 \begin{itemize}
@@ -498,12 +510,6 @@ General output directory organization is  :
 
 \section{Output files samples}
 \subsection{1-point POP}
-%\lstinputlisting[%numbers=left,
-		%frame=single,
-		%breaklines=false,
-		%caption={[1-point output file] 1-point output file (selected lines from my\_name.pedigree-and-probabilities.M_1_1.csv from my\_directory/my\_name.1-point/)},
-		%linerange={1-12,107-112}
-%		]
 \lstinputlisting[numbers=left,
 		frame=single,
 		caption={[1-point output file] 1-point output file (selected lines from file \texttt{my\_name.pedigree-and-probabilities.M\_1\_1.csv}  in directory \texttt{my\_directory/my\_name.1-point/} )  },%(selected lines from my\_name.pedigree-and-probabilities.M_1_1.csv from my\_directory/my\_name.1-point/)},
@@ -512,6 +518,8 @@ General output directory organization is  :
 
 Note that you must use \texttt{-01} command line option in \texttt{spell-marker} in order to generate these files. 
 
+\subsection{n-point POP}
+
 
 \begin{appendices}